What sort of lacquer are you applying? Spray or wipe-on?

Most stains are soluble in water and spirits, so if wiping or rubbing on the lacquer, I'd be careful not to push hard on the surface for the first coat or two as you might loosen some of the stain and make it look patchy. A brush would be better than a cloth in this situation. You can get sponge brushes, which seem to do a good job and don't leave the ridge-marks that a brush leaves.

If spraying, you're fine.